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Combined antrum and corpus biopsy protocol improves Helicobacter pylori culture success

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World Journal of Gastrointestinal Pathophysiology 2022年第1期13卷 34-40页

作者： Denise E Brennan Colm O'morain Deirdre mcNamara Sinead m smith Department of Clinical medicine Trinity College DublinTrinity CentreTallaght University HospitalDublin D24Ireland

BACKGROUND Helicobacter pylori(***)causes chronic gastritis,peptic ulcer disease,gastric adenocarcinoma and mucosa-associated lymphoid tissue *** rates have fallen,mainly due to antimicrobial *** guidelines recommend that first-line treatment is based on the local prevalence of antimicrobial resistance and that rescue therapies are guided by antimicrobial susceptibility testing(AST).However,*** culture is challenging and culture-based AST is not routinely performed in the majority of *** of *** culture from clinical specimens will enable more widespread AST to determine the most appropriate antimicrobials for *** *** To determine whether dual antrum and corpus biopsy sampling is superior to single antrum biopsy sampling for *** *** The study received ethical approval from the joint research ethics committee of Tallaght University Hospital and ***’s *** referred for upper gastrointestinal endoscopy were invited to *** were collected in tubes containing Dent’s transport medium and patient demographics were *** were used to inoculate Colombia blood agar *** were incubated under microaerobic conditions and evaluated for the presence of *** analyses were performed using Graphpad *** variables were compared using the two-tailed independent *** variables were compared using the two-tailed Fisher exact *** all cases,a P value less than 0.05 was considered *** In all,samples from 219 ***-infected patients were analysed in the *** mean age of recruited patients was 48±14.9 years and 50.7%(n=111)were *** most common endoscopic finding was gastritis(58.9%;n=129).Gastric ulcer was diagnosed in 4.6%(n=10)of patients,while duodenal ulcer was diagnosed in 2.7%(n=6).Single antrum biopsies were collected from 73 patients,whereas combined antrum

关键词： Helicobacter pylori Culture Antimicrobial susceptibility testing Antimicrobial Antrum Corpus

Out of step： The function of TALE homeodomain transcription factors that regulate shoot meristem maintenance and meristem identity

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Frontiers in Biology 2012年第2期7卷 144-154页

作者： Shang WU Harley m. S. smith Center for Plant Cell Biology Institute of Integrative Genome Biology Department of Botany and Plant Sciences University of CaliforniaRiverside CA 92521 USA

The indeterminate growth pattern displayed by shoots is mediated by the proper maintenance of the shoot meristem. meristem maintenance is dependent upon the balance of stem cell perpetuation in the central zone （CZ） and organogenesis in the peripheral zone （PZ）. Although the mechanisms that coordinate CZ and PZ function is not understood, meristem cell fate is likely achieved by the spatial interplay between gene regulatory networks and hormone signaling pathways. During shoot maturation, the identity of the shoot meristem as well as the lateral organs are transformed during the vegetative and reproductive transitions. Studies in model plant systems indicate that three amino acid extension （TALE） homeodomain proteins integrate signaling events that transform the identity of the shoot meristem and establish reproductive patterns of growth. This review will highlight the function of TALE homeodomain transcription factors that regulate shoot meristem cell fate and also function with phase specific regulators to maintain shoot meristem identity.

关键词： shoot development meristem flowering patterning homeodomain

Leaf/shoot level ecophysiology in two broadleaf and two needle-leaf species under representative cloud regimes at alpine treeline

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Journal of Plant Ecology 2016年第6期9卷 762-772页

作者： Adriana Sanchez Nicole m.Hughes William K.smith Programa de Biología Universidad del RosarioCarrera 24 No.63C-69BogotáDC 110011Colombia Department of Biology Wake Forest University136 Winston HallWinston-SalemNC 27106USA Department of Biology High Point UniversityUniversity Station 3591High PointNC 27262USA

Aims The effects of clouds are now recognized as critically important to the understanding of climate change impacts on ***,few studies have focused specifically on the ecophysiological responses of plants to *** continental mountain ranges are characterized by common convective cloud formation in the afternoons,yet little is known regarding this influence on plant water and carbon *** we compare the ecophysiology of two contrasting,yet ubiquitous growth forms,needle-leaf and broadleaf,under representative cloud regimes of the Snowy Range,medicine Bow mountains,southeastern Wyoming,*** Photosynthetic gas exchange,water use efficiency,xylem water potentials and micrometeorological data were measured on representative clear,overcast and partly cloudy days during the summers of 2012 and 2013 for two indigenous broadleaf(Caltha leptosepala and Arnica parryi)and two needle-leaf species(Picea engelmannii and Abies lasiocarpa)that co-occur *** Findings Reductions in sunlight with cloud cover resulted in more dramatic declines in photosynthesis for the two broadleaf species(ca.50-70%reduction)versus the two conifers(no significant difference).In addition,the presence of clouds corresponded with lower leaf conductance,transpiration and plant water status in all ***,the more constant photosynthesis in conifers under all cloud conditions,coupled with reduced transpiration,resulted in greater water use efficiency(ca.25%higher)than the broadleaf *** differences appear to implicate the potential importance of natural cloud patterns in the adaptive ecophysiology of these two contrasting,but common,plant growth forms.

关键词： gas exchange light response curves water use efficiency xylem water potential

Does variable stand structure associated with multi-cohort forests support diversity of ground beetle (Coleoptera, Carabidae) communities in the central Nearctic boreal forest？

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Journal of Forestry Research 2016年第5期27卷 1191-1202页

作者： Erica P. Barkley Jay R. malcolm Sandy m. smith m. Isabel Bellocq Faculty of Forestry University of Toronto 33 Willcocks Street Toronto ON M5S 3B3 Canada Departamento de Ecología Genética y Evolución IEGEBA(CONICET-UBA) Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires Buenos Aires Argentina

multi-cohort management （mCm） that retains a range of stand structures （age and size class） has been proposed to emulate natural disturbance and improve management in the Nearctic boreal forest. Although mCm forests contain both single- and multi-aged stands of mixed tree sizes, little is known about how variable stand structure affects associated fauna and biodiversity. Here, we examine the relationship between ground beetle （Coleoptera, Carabidae） communities and stand characteristics across a range of forest structure （=cohort classes）. Given that mCm classes are defined by the distribution of their tree-stem diameters, we ask whether parameters associated with these distributions （Weibull） could explain observed variation in carabid communities, and if so, how this compares to traditional habitat variables such as stand age, foliage complexity or volume of downed woody debris. We sampled carabids using weekly pitfall collections and compared these with structural habitat variables across a range of cohort classes （stand structure and age since disturbance） in 18 sites of upland mixed boreal forests from central Canada. Results showed that richness and diversity of carabid communities were similar among cohort classes. Weibull parameters from the diameter distribution of all stems were the strongest predictors of variation in carabid communities among sites, but vertical foliage complexity, understory thickness, and percentage of deciduous composition were also significant. The abundance of several carabid forest specialists was strongly correlated with tree canopy height, the presence of large trees, and high vertical foliage complexity. Our results demonstrate that variable forest structure, as expected under mCm, may be useful in retaining the natural range of ground beetle species across the central Nearctic boreal forest.

关键词： Biodiversity conservation Boreal forest Carabidae Forest structure Ground beetles multi-cohortmanagement Tree diameter distribution

The spatial dynamics of Ukraine air quality impacted by the war and pandemic

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International Journal of Digital Earth 2023年第1期16卷 3680-3705页

作者： vizhi Qian Liu Theodore S.Trefonidesc Sina Hasheminassab Jennifer smith Thomas Huang Kevin m.marlis Joe T.Roberts Zifu Wang Dexuan Sha Ana Beatriz moura Pereira Heramb Podar Jacob Cain Chaowei Yang Department of Geography and GeoInformation Science George Mason UniversityFairfaxVAUSA Jet Propulsion Laboratory California Institute of TechnologyPasaden1CAUSA Dartmouth College HanoverNHUSA Bayer WashingtonDCUSA Northern Virginia Community College AnnandaleVAUSA Indian Institute of Technology RoorkeeIndia

In recent years,our world has experienced significant disruptions due to the COviD-19 pandemic,and Russia's 2022 invasion of Ukraine,impacting human activities and the global *** paper explored air quality changes in Ukraine due to COVID-19,and Russia's invasion of Ukraine using on-demand with a what-you-see-is-what-you-get *** the cOVID-19 pandemic,strict quarantine policies in Ukraine led to a 2%reduction in tropospheric NO_(2) concentration before the lockdown and 4%during the lockdown *** like Kyiv,Donetsk,and Dnipro exhibited reductions of 5%,11%,and 16%,*** SO_(2) column concentration decreased by 6%before the lockdown and 2.5%during the lockdown period,except in high population density *** showed the highest reduction of 17%in SO_(2) concentration,while Donetsk and Dnipro exhibited an 11%***,during the Russian invasion,there was a significant increase in tropospheric NO_(2) concentration in heavily destroyed Kharkiv while most eastern regions experienced a *** total SO_(2) column was 48%higher before the war but reduced throughout the country after the war,except for in Kyiv and a few central *** findings can contribute to analyzing air pollution and building digital twin simulations for future reconstruction scenarios.

关键词： ukraine war air pollution pandemic climate change environment spatiotemporal computing digital twins

DEEP-UV CONFOCAL FLUORESCENCE ImAGING AND SUPER-RESOLUTION OPTICAL mICROSCOPY OF BIOLOGICAL SAmPLES

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Journal of Innovative Optical Health Sciences 2012年第4期5卷 24-32页

作者： TREVOR A.smith LIISA m.HIRVONEN CRAIG N.LINCOLN XIAOTAO HAO School of Chemistry and ARC Centre of Excellence for Coherent X-ray Science University of Melbourne Parkville 3010Australia

A wide range of techniques has been developed to image biological samples at high spatial and temporal *** this paper,we report recent results from deep-UV confocal fAuorescence microscopy to image inherent emission from fuorophores such as tryptophan,and structured ilumination microscopy(SIm)of biological *** motivation for developing deep-UV fhuorescence imaging and SIm is to provide methods to complement our measurements in the emerging field of X-ray coherent diffractive imaging.

关键词： Time resolved fuorescence imaging structured ilumnina tion microscopy

Collision tumor of the kidney composed of clear cell carcinoma and collecting duct carcinoma: report of a case with unusual morphology and clinical follow-up

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Chinese Journal of Cancer 2014年第7期33卷 351-355页

作者： Rhonda Burch-smith Nizar m Tannir Erika Resetkova Pheroze Tamboli Priya Rao Department of Pathology MD Anderson Cancer Center Department of Geni-tourinary medical Oncology MD Anderson Cancer Center

We report the case of a 67-year-old female who presented with a large renal mass. Gross examination of the nephrectomy specimen demonstrated a 6-cm renal mass that invaded into the renal sinus and perinephric fat. Histologic examination revealed two distinct tumor types. The first type was a conventional(clear cell) renal cell carcinoma that was of low nuclear grade and comprised the minority of the overall tumor. The second type was a high-grade collecting duct carcinoma with glandular/tubular differentiation and composed the majority of the tumor. Immunohistochemical studies demonstrated distinctive patterns of the two tumor types, thus confirming two distinct lineages. Five months postoperatively, the patient developed metastasis to the lungs and right hilar lymph node region. A fine needle aspiration of a lung nodule demonstrated a metastatic, poorly differentiated carcinoma, similar to the collecting duct carcinoma component in the kidney. Collision tumors of the kidney are rare with fewer than 10 cases reported in the literature. Our report further expands the spectrum of this rare phenomenon.

关键词：集合管肾细胞肾脏肿瘤病例报告癌组织学检查随访

Chemosensory response in stunted prairie rattlesnakes Crotalus viridis viridis

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Current Zoology 2013年第2期59卷 175-179页

作者： Anthony J. SAVIOLA David CHISZAR Hobart m. smith Stephen EmACKESSY School of Biological Sciences University of Northern Colorado Greeley CO 80639 USA. Department of Psychology University of Colorado Boulder Colorado 80309 USA Department of Ecology and Evolutionary Biology University of Colorado Boulder CO 80309 USA

Rattlesnakes use chemical stimuli in ambush site selection and for relocation of envenomated prey through strike-induced chemosensory searching. Shifts in responsiveness to prey chemicals have been documented in many snakes, and often correlate with prey commonly taken as snakes increase in age and size as well as geographical locations of the species. For instance, neonate rattlesnakes that prey primarily on ectotherms responded most strongly to chemical cues of commonly taken lizard prey, whereas adult rattlesnakes that prey primarily on small mammals responded significantly to chemical cues of commonly taken rodents. In the current study, 11 Prairie RattlesnakesCrotalus viridis viridiswhich were classified as large neonates based on measures of snout-vent length (SVL) and body mass, yet chronologically were at or near adulthood, were tested for their responsiveness to chemical extracts of natural and non-natural prey items. Although the snakes had eaten only neonate lab mice (mus musculus), they responded significantly more to chemical cues of natural prey items and particularly to chemical cues of prey normally taken by subadults (Peromyscusmice andSceloporuslizard). These results suggest that ontogenetic shifts in responsiveness to natural prey chemical cues are innately programmed and are not based on body size or feeding experience inC. v. viridis. This does not imply, however, that growth and experience are without effects, especially with novel prey or rare prey that have experienced recent population expansion.

关键词：化学感受化学反应响尾蛇贻贝发育不良草原天然提取物小型哺乳动物

Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

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Genomics, Proteomics & Bioinformatics 2007年第3期5卷 256-259页

作者： Edward m.smith Jack Littrell michael Olivier Human and molecular Genetics Center Medical College of WisconsinMilwaukeeWI 53226USA.

High-throughput SNP genotyping platforms use automated genotype calling algorithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been optimized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be advisable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

关键词： clustering SNP genotyping algorithm